Large-scale emergency assistance programmes in Somalia use a variety of transfer modalities including in-kind food provision, food vouchers, and cash transfers. Evidence is needed to better understand whether and how such modalities differ in reducing the risk of acute malnutrition in vulnerable groups, such as the 800,000 pregnant and lactating women affected by the 2017/18 food crisis. Methods Changes in diet and acute malnutrition status were assessed among pregnant and lactating women receiving similarly sized household transfers over a four-month period (total value of ~US$450 per household) delivered either as food vouchers or as mixed transfers consisting of in-kind food, vouchers, and cash. Baseline and endline comparisons were conducted for 514 women in Wajid, Somalia. Primary study outcomes were Minimum Dietary Diversity for Women, meal frequency, and mid-upper arm circumference (MUAC), with MUAC<21.0 cm classified as acute malnutrition. Adjusted analyses consisted of difference- in-difference analysis using linear and logistic regression models with inverse probability weighting based on propensity scores to account for the non-randomized design. Findings No significant difference in change in dietary quality was observed between food voucher and mixed transfer recipients; a significant difference in change in mean meal frequency was observed (0.3 meals/day, CI: 0.1-0.5, p = 0.001) and the mixed transfer group had significantly greater meal frequency at endline (p<0.001). Mean MUAC increased significantly among both voucher (0.9cm, CI: 0.6-1.3, p = 0.001) and mixed transfer recipients (1.3cm, CI: 1.1-1.5, p = 0.001) over the intervention period in adjusted analysis, however, the difference in magnitude of change between the two groups was not statistically significant (0.4cm, CI: -0.1-0.08, p = 0.086). Conclusions Within the context of the 2017/18 Somalia food crisis, the modality of assistance provided to pregnant and lactating women (mixed transfers or food-vouchers) made no difference in preventing acute malnutrition and protecting nutritional status.